imadoc2struct

'imadoc2struct': reads the xml file for image documentation 

function [s,errormsg]=imadoc2struct(ImaDoc) 
--------------------------------------------------------
 OUTPUT:
 s: structutre representing ImaDoc
 errormsg: error message

 INPUT:
 ImaDoc: full name of the xml input file with head key ImaDoc

0001 %'imadoc2struct': reads the xml file for image documentation
0002 %
0003 %function [s,errormsg]=imadoc2struct(ImaDoc)
0004 %--------------------------------------------------------
0005 % OUTPUT:
0006 % s: structutre representing ImaDoc
0007 % errormsg: error message
0008 %
0009 % INPUT:
0010 % ImaDoc: full name of the xml input file with head key ImaDoc
0011 
0012 function [s,errormsg]=imadoc2struct(ImaDoc) 
0013 s=[];
0014 errormsg=[];%default
0015 try
0016     t=xmltree(ImaDoc);
0017 catch
0018     errormsg={[ImaDoc ' is not a valid xml file']; lasterr};
0019     display(errormsg);
0020     return
0021 end
0022 RootKey=get(t,1,'name');
0023 if ~isequal(RootKey,'ImaDoc')
0024     errormsg=[ImaDoc ' is not an image documentation file'];
0025     return
0026 end      
0027 s=convert(t);
0028 s.Time=[];%default
0029 if isfield(s,'Camera')
0030     if isfield(s.Camera,'BurstTiming')
0031         s.Time=get_time(s.Camera.BurstTiming);
0032         s.Camera=rmfield(s.Camera,'BurstTiming');
0033     end
0034 end
0035 if isfield(s,'GeometryCalib')
0036     s.GeometryCalib=get_GeometryCalib(s.GeometryCalib);
0037 end 
0038 
0039 %----------------------------------------
0040 function abs_time=get_time(BurstTiming)
0041 abs_time=[];
0042 for k=1:length(BurstTiming)
0043      
0044     Frequency=1;%default
0045     if isfield(BurstTiming,'FrameFrequency')&&~isempty(BurstTiming.FrameFrequency)
0046         Frequency=str2double(BurstTiming.FrameFrequency);
0047     end
0048     
0049     Dtj=[];%default
0050     if isfield(BurstTiming,'Dtj')
0051        Dtj=str2num(BurstTiming.Dtj);
0052     end
0053     
0054     NbDtj=1;%default
0055     if isfield(BurstTiming,'NbDtj')&&~isempty(BurstTiming.NbDtj)
0056         NbDtj=str2double(BurstTiming.NbDtj);
0057     end
0058     Dti=[]; %default
0059     if isfield(BurstTiming,'Dti')  
0060         Dti=str2num(BurstTiming.Dti);
0061     end
0062     
0063     NbDti=1;%default
0064     if isfield(BurstTiming,'NbDti')&&~isempty(BurstTiming.NbDti)  
0065        NbDti=str2double(BurstTiming.NbDti);
0066     end   
0067     if ~isempty(Dtj)
0068         Dtj=reshape(Dtj'*ones(1,NbDtj),1,length(Dtj)*NbDtj);
0069     end
0070     Dtj=[0 Dtj];
0071     dtunit=Dtj/Frequency;   
0072     Time=[];%default
0073     if isfield(BurstTiming,'Time') && ~isempty(BurstTiming.Time)
0074         %nbfield=length(BurstTiming.Time)
0075         if ischar(BurstTiming.Time)
0076              Time(1,1)=str2num(BurstTiming.Time);
0077              nbfield=1;
0078         else
0079             nbfield=length(BurstTiming.Time);
0080              for itime=1:nbfield   
0081                  Time(itime,1)=str2num(BurstTiming.Time{itime});
0082              end
0083         end
0084         abstime_read=Time*ones(1,length(Dtj))+ones(nbfield,1)*cumsum(dtunit);
0085         abs_time=[abs_time;abstime_read];
0086         if ~isempty(Dti) && size(abs_time,1)==1
0087            abs_time=ones(NbDti+1,1)*abs_time+(Dti/Frequency)*(0:NbDti)'*ones(size(abs_time));
0088         end
0089     end
0090 end
0091 
0092 %----------------------------------------------------------------
0093 function tsai=get_GeometryCalib(s)
0094 %default values:
0095 tsai.f=1;
0096 tsai.dpx=1;
0097 tsai.dpy=1;
0098 tsai.sx=1;
0099 tsai.Cx=0;
0100 tsai.Cy=0;
0101 tsai.Tx=0;
0102 tsai.Ty=0;
0103 tsai.Tz=1;
0104 tsai.R=[1 0 0; 0 1 0; 0 0 0];
0105 tsai.kappa1=0;
0106 if isfield(s,'focal')
0107     tsai.f=str2double(s.focal);
0108 end
0109 if isfield(s,'dpx_dpy')
0110     dpx_dpy=str2num(s.dpx_dpy);
0111     tsai.dpx=dpx_dpy(1);
0112     tsai.dpy=dpx_dpy(2);
0113 end
0114 if isfield(s,'sx')
0115     tsai.sx=str2double(s.sx);
0116 end
0117 if isfield(s,'Cx_Cy')
0118     Cx_Cy=str2num(s.Cx_Cy);
0119     tsai.Cx=Cx_Cy(1);
0120     tsai.Cy=Cx_Cy(2);
0121 end
0122 if isfield(s,'Tx_Ty_Tz')
0123     Tx_Ty_Tz=str2num(s.Tx_Ty_Tz);
0124     tsai.Tx=Tx_Ty_Tz(1);
0125     tsai.Ty=Tx_Ty_Tz(2);
0126     tsai.Tz=Tx_Ty_Tz(3);
0127 end
0128 if isfield(s,'R')
0129     tsai.R=[str2num(s.R{1});str2num(s.R{2});str2num(s.R{3})];
0130 end
0131 if isfield(s,'kappa1')
0132     tsai.kappa1=str2double(s.kappa1);
0133 end
0134 if isfield(s,'SliceOrigin')
0135     if ischar(s.SliceOrigin)
0136         tsai.SliceOrigin=str2num(s.SliceOrigin);
0137     end
0138 end
0139 if isfield(s,'SliceDZ')
0140 %     SliceOrigin=0;
0141 %     SliceOZ=1;%default
0142     NbSlice=1;%default
0143     if ischar(s.NbSlice)
0144         NbSlice=str2double(s.NbSlice);
0145     end
0146     if ischar(s.SliceOrigin)
0147         SliceOrigin=str2num(s.SliceOrigin);
0148         if length(SliceOrigin)==3
0149             tsai.SliceCoord(1,:)=SliceOrigin;%to generalize for angles
0150         end
0151     end
0152     if ischar(s.SliceDZ)
0153         SliceOZ=str2double(s.SliceDZ); 
0154         tsai.SliceCoord=tsai.SliceZ+SliceOZ*(0:NbSlice-1);
0155     end
0156     if iscell(s.SliceDZ)
0157         for j=1:length(s.SliceDZ)
0158             tsai.SliceCoord(j,:)=tsai.SliceZ(j-1,:)+str2num(s.SliceDZ{j});
0159         end
0160     end
0161 end
0162 if isfield(s,'PlanePos')%Obsolete
0163     if ischar(s.PlanePos)
0164         tsai.SliceCoord(1,:)=str2num(s.PlanePos);
0165     else
0166         for j=1:length(s.PlanePos)
0167             PlanePos=str2num(s.PlanePos{j});
0168             tsai.SliceCoord(j,:)=PlanePos;
0169         end
0170     end
0171 end
0172 
0173 %look for laser plane definitions
0174 
0175 
0176 
0177